GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutB in Bacillus altitudinis 41KF2b

Align Lactate utilization protein B (characterized)
to candidate WP_035700907.1 BA79_RS03525 iron-sulfur cluster-binding protein

Query= SwissProt::Q81GA4
         (473 letters)



>NCBI__GCF_000691145.1:WP_035700907.1
          Length = 474

 Score =  742 bits (1915), Expect = 0.0
 Identities = 357/470 (75%), Positives = 413/470 (87%), Gaps = 1/470 (0%)

Query: 1   MSMKISEKKFNDRVGDGIQDSFMRGAVSSAQTRLYTNRLKAADELGNWEEWRELGEQIRQ 60
           MSMKI EK F +R+G+G++D+ MRGAVSSAQ RLY  R+ A++ LGNWE+WRELGE IRQ
Sbjct: 1   MSMKIGEKAFKERIGEGLEDAVMRGAVSSAQERLYKRRMTASEVLGNWEKWRELGEDIRQ 60

Query: 61  HTLENLDYYLMQLSENVSKRGGHVYFAKTKEEAAKYIQDVAKKKQAKKVVKSKSMVTEEI 120
           HTL +LD YL QLSE+VS+RGGHV+FAKTKEEA+ YIQDVA+KK AKK+VKSKSMVTEEI
Sbjct: 61  HTLAHLDDYLYQLSESVSRRGGHVFFAKTKEEASAYIQDVAQKKAAKKIVKSKSMVTEEI 120

Query: 121 SMNHALEEIGCEVLESDLGEYILQVDN-DPPSHIIAPALHKNRTQIRDVFKEKLGYENSD 179
            MN ALEEIGCEV+ESDLGEYILQVD+ +PPSHI+APALH  + QIR+VF EKLGY+ S+
Sbjct: 121 EMNQALEEIGCEVVESDLGEYILQVDDHEPPSHIVAPALHMTKEQIREVFHEKLGYDMSE 180

Query: 180 DPYEMTKFVRKQLREKFMDAEIGVTGCNFAVANTGSLCLVTNEGNADLVMSIPKTQIAVM 239
            P EMTKFVR  LREKF++A+IGVTGCNFAVA+TGS+CLVTNEGNADLV SIPKT IAVM
Sbjct: 181 TPEEMTKFVRALLREKFLEADIGVTGCNFAVADTGSICLVTNEGNADLVTSIPKTHIAVM 240

Query: 240 GMERMVPTMEELDVLVGLLCRSAVGQKLTSYVTVAGPIQEEEVDGPEEFHLVVVDNGRSQ 299
           GMER+VPT EELDVLVGLLCRSAVGQKLTSY++V GP  E EVDGPEEFHLV+VDNGRS 
Sbjct: 241 GMERLVPTTEELDVLVGLLCRSAVGQKLTSYISVVGPKGEGEVDGPEEFHLVIVDNGRST 300

Query: 300 ILGSEFRSVLQCIRCAACVNVCPVYRHVGGHSYGSIYSGPIGAVLTPLLGGYDDYKELPY 359
           ILG+EF+ VLQCIRCAAC+NVCPVYRHVGGHSYGSIY GPIGAVL+PLLGGYDDY+ELP+
Sbjct: 301 ILGTEFQPVLQCIRCAACINVCPVYRHVGGHSYGSIYPGPIGAVLSPLLGGYDDYQELPF 360

Query: 360 ASSLCGACTEACPVKIPLHDLLLKHRQVIVEQEGRAPLAEKLAMKMFSMGASSAALYKMG 419
           ASSLC ACT+ACPVKIPLH+LL+KHRQVIVE+EGRAP AE +AMKMF MGAS+  +Y+ G
Sbjct: 361 ASSLCAACTDACPVKIPLHELLIKHRQVIVEKEGRAPKAEMMAMKMFGMGASTPRMYRFG 420

Query: 420 SKMAPAAMSPFTSGNRVSKGVGPLKNWTDIREFPAPSKERFRDWYKDHKK 469
           +K AP  +    S  ++SKG GPLKNWT+IR+ PAPSKERFRDW+K  +K
Sbjct: 421 TKAAPVLLKRMASNGQISKGAGPLKNWTEIRDLPAPSKERFRDWFKKKQK 470


Lambda     K      H
   0.317    0.133    0.391 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 757
Number of extensions: 29
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 473
Length of database: 474
Length adjustment: 33
Effective length of query: 440
Effective length of database: 441
Effective search space:   194040
Effective search space used:   194040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory